Receptor
PDB id Resolution Class Description Source Keywords
3V7Y 1.97 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH 5'-N-PROPARGYLAMINO-5'-DEOXYADENOSINE LISTERIA MONOCYTOGENES LIGAND-SCREENING BY CRYSTALLOGRAPHY TWO-DOMAIN KINASE INORPOLYPHOSPHATE/ATP-NAD KINASE 1 TRANSFERASE
Ref.: SCREENING AND IN SITU SYNTHESIS USING CRYSTALS OF A KINASE LEAD TO A POTENT ANTISTAPHYLOCOCCAL COMPOUND STRUCTURE V. 20 1107 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A3N A:302;
A:303;
Valid;
Valid;
none;
none;
submit data
304.305 C13 H16 N6 O3 C#CCN...
CIT A:301;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DHU 2.33 Å EC: 2.7.1.23 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENE COMPLEX WITH A NOVEL INHIBITOR LISTERIA MONOCYTOGENES SEROVAR 1/2A (SATCC BAA-679 / EGD-E) TETRAMERIC NAD KINASE TRANSFERASE
Ref.: 8-THIOALKYL-ADENOSINE DERIVATIVES INHIBIT LISTERIA MONOCYTOGENES NAD KINASE THROUGH A NOVEL BINDING MO EUR.J.MED.CHEM. V. 124 1041 2016
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3V7Y - A3N C13 H16 N6 O3 C#CCNC[C@@....
2 2Q5F Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
3 3V8M - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
4 3V8P - ZNB C22 H26 Br N14 O7 S c1nc(c2c(n....
5 3V7W - ZAS C10 H13 N8 O3 c1nc(c2c(n....
6 4DY6 - A22 C20 H27 N10 O16 P3 c1nc(c2c(n....
7 3V80 - AOC C13 H15 N5 O4 C#CCOC[C@@....
8 2I2A Ki = 0.04 mM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 2I2D - A2D C20 H26 N10 O13 P2 c1nc(c2c(n....
10 5DHQ Ki = 2 uM 5AK C20 H23 Br N6 O5 S c1cc(cc(c1....
11 3V8R - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
12 2I2C Ki = 0.02 mM DTA C20 H24 N10 O6 S2 c1nc(c2c(n....
13 2I2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 2I29 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 3V8Q - 5N5 C10 H14 N6 O3 c1nc(c2c(n....
16 2I2B - CC5 C9 H11 N5 O3 c1nc(c2c(n....
17 5DHR Ki = 23 uM 5AJ C21 H23 N11 O4 S c1ccc2c(c1....
18 3V8N - 5NB C10 H13 Br N6 O3 c1nc(c2c(n....
19 5DHP Ki = 140 uM 5AQ C20 H24 N6 O5 S c1ccc(cc1)....
20 5DHU Ki = 0.5 uM 5A8 C22 H24 N10 O4 S c1ccc2c(c1....
21 3V7U - MTA C11 H15 N5 O3 S CSC[C@@H]1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A3N; Similar ligands found: 246
No: Ligand ECFP6 Tc MDL keys Tc
1 A3N 1 1
2 ADN 0.651515 0.923077
3 XYA 0.651515 0.923077
4 RAB 0.651515 0.923077
5 AOC 0.64 0.924242
6 5N5 0.632353 0.953125
7 A4D 0.623188 0.923077
8 5CD 0.623188 0.878788
9 EP4 0.597222 0.869565
10 M2T 0.589041 0.819444
11 DTA 0.589041 0.828571
12 3DH 0.586667 0.867647
13 6RE 0.584416 0.821918
14 MTA 0.581081 0.867647
15 AMP 0.571429 0.783784
16 LMS 0.571429 0.690476
17 A 0.571429 0.783784
18 J7C 0.56962 0.833333
19 SRA 0.564103 0.74359
20 GJV 0.5625 0.810811
21 ZAS 0.551282 0.830986
22 5AD 0.550725 0.815385
23 ABM 0.55 0.763158
24 A2D 0.55 0.786667
25 45A 0.55 0.763158
26 5AS 0.548781 0.689655
27 DSH 0.5375 0.859155
28 BA3 0.536585 0.786667
29 AP2 0.536585 0.75641
30 A12 0.536585 0.75641
31 AU1 0.535714 0.766234
32 ADP 0.53012 0.786667
33 AP5 0.53012 0.786667
34 B4P 0.53012 0.786667
35 S4M 0.52439 0.782051
36 SON 0.52381 0.734177
37 AN2 0.52381 0.776316
38 AT4 0.52381 0.75641
39 ADP MG 0.52381 0.783784
40 MAO 0.518072 0.75
41 M33 0.517647 0.776316
42 ADX 0.517647 0.710843
43 CA0 0.517647 0.766234
44 MHZ 0.517647 0.772152
45 ACP 0.511628 0.766234
46 50T 0.511628 0.776316
47 ATP 0.511628 0.786667
48 SFG 0.511628 0.814286
49 HEJ 0.511628 0.786667
50 H1Q 0.511628 0.773333
51 KG4 0.511628 0.766234
52 G5A 0.511364 0.689655
53 A7D 0.505882 0.869565
54 APC 0.505747 0.75641
55 AR6 0.505747 0.786667
56 AQP 0.505747 0.786667
57 PRX 0.505747 0.74359
58 5FA 0.505747 0.786667
59 APR 0.505747 0.786667
60 ANP 0.505618 0.766234
61 ADV 0.5 0.75641
62 Y3J 0.5 0.791045
63 APC MG 0.5 0.763158
64 ATP MG 0.5 0.783784
65 7D7 0.5 0.808824
66 RBY 0.5 0.75641
67 ADP PO3 0.5 0.783784
68 AGS 0.5 0.746835
69 SAP 0.5 0.746835
70 AD9 0.5 0.766234
71 8X1 0.494624 0.666667
72 A5A 0.494505 0.674419
73 5X8 0.494253 0.855072
74 VO4 ADP 0.48913 0.753247
75 ADP VO4 0.48913 0.753247
76 SSA 0.48913 0.689655
77 T99 0.488889 0.75641
78 ACQ 0.488889 0.766234
79 TAT 0.488889 0.75641
80 GAP 0.488889 0.789474
81 54H 0.483871 0.659091
82 52H 0.483871 0.651685
83 VMS 0.483871 0.659091
84 5AL 0.483516 0.753247
85 8LE 0.483516 0.725
86 SA8 0.483146 0.810811
87 A5D 0.483146 0.828571
88 NEC 0.481928 0.865672
89 A3G 0.481928 0.897059
90 3AM 0.481481 0.77027
91 53H 0.478723 0.651685
92 TSB 0.478723 0.686047
93 MAP 0.478723 0.746835
94 5CA 0.478723 0.689655
95 ATF 0.478261 0.75641
96 ADP ALF 0.478261 0.725
97 ALF ADP 0.478261 0.725
98 SAH 0.477778 0.830986
99 SAI 0.477778 0.819444
100 OOB 0.473684 0.753247
101 9ZA 0.473684 0.716049
102 9ZD 0.473684 0.716049
103 SRP 0.473118 0.75641
104 S7M 0.473118 0.766234
105 8LH 0.473118 0.75641
106 6YZ 0.473118 0.766234
107 SAM 0.472527 0.766234
108 P5A 0.469388 0.659341
109 NSS 0.46875 0.670455
110 ADQ 0.46875 0.789474
111 DSZ 0.46875 0.670455
112 0UM 0.46875 0.8
113 LSS 0.46875 0.637363
114 4AD 0.46875 0.746835
115 HQG 0.468085 0.776316
116 EEM 0.467391 0.766234
117 AAT 0.467391 0.835616
118 N5O 0.464286 0.855072
119 DLL 0.463918 0.753247
120 00A 0.463918 0.716049
121 NVA LMS 0.463918 0.630435
122 AHX 0.463918 0.75
123 DAL AMP 0.463158 0.753247
124 8LQ 0.463158 0.734177
125 A22 0.463158 0.776316
126 LEU LMS 0.459184 0.630435
127 ADP BMA 0.459184 0.789474
128 S8M 0.458333 0.797297
129 OZV 0.458333 0.786667
130 25A 0.458333 0.763158
131 5SV 0.458333 0.707317
132 8QN 0.458333 0.753247
133 SMM 0.457447 0.7375
134 GSU 0.454545 0.651685
135 KAA 0.454545 0.666667
136 A A 0.454545 0.763158
137 3AD 0.454545 0.878788
138 B5V 0.454545 0.734177
139 A3S 0.454545 0.882353
140 AMO 0.453608 0.75641
141 PAJ 0.453608 0.740741
142 A3R 0.453608 0.782051
143 A1R 0.453608 0.782051
144 N5A 0.453488 0.852941
145 2AM 0.451219 0.783784
146 B5M 0.45098 0.725
147 YLA 0.45045 0.746988
148 JB6 0.45 0.716049
149 PTJ 0.45 0.707317
150 BIS 0.45 0.7375
151 NB8 0.45 0.728395
152 TXA 0.45 0.75641
153 8Q2 0.449541 0.685393
154 A3P 0.448276 0.76
155 YSA 0.446602 0.651685
156 3UK 0.444444 0.74359
157 9X8 0.444444 0.746835
158 A3T 0.444444 0.895522
159 OAD 0.444444 0.766234
160 GEK 0.443299 0.797297
161 AMP DBH 0.442308 0.766234
162 4UV 0.442308 0.746835
163 WAQ 0.44 0.716049
164 PR8 0.44 0.731707
165 LAD 0.44 0.740741
166 CC5 0.44 0.863636
167 7D5 0.439024 0.727273
168 FA5 0.436893 0.734177
169 8PZ 0.436893 0.670455
170 YAP 0.436893 0.725
171 FYA 0.435644 0.753247
172 9K8 0.435644 0.630435
173 3OD 0.435644 0.766234
174 1ZZ 0.435644 0.682353
175 ME8 0.435644 0.702381
176 SXZ 0.435644 0.766234
177 OVE 0.435294 0.753247
178 62X 0.434343 0.759494
179 4UU 0.433962 0.746835
180 XAH 0.432692 0.722892
181 B1U 0.432692 0.617021
182 MYR AMP 0.431373 0.682353
183 25L 0.431373 0.776316
184 K15 0.43 0.779221
185 A6D 0.43 0.734177
186 QQX 0.428571 0.705128
187 9SN 0.427184 0.707317
188 QQY 0.423529 0.714286
189 RP1 0.423529 0.717949
190 SP1 0.423529 0.717949
191 ACK 0.423529 0.753425
192 B5Y 0.423077 0.725
193 ATP A 0.423077 0.773333
194 ATP A A A 0.423077 0.773333
195 YLP 0.422018 0.705882
196 BS5 0.421053 0.67033
197 AFH 0.420561 0.740741
198 7MD 0.420561 0.743902
199 ARG AMP 0.420561 0.714286
200 PAP 0.419355 0.773333
201 D3Y 0.418367 0.857143
202 4UW 0.418182 0.719512
203 NAI 0.418182 0.759494
204 3L1 0.417722 0.84058
205 3D1 0.417722 0.84058
206 MTP 0.417722 0.791667
207 KB1 0.417476 0.8
208 KH3 0.416667 0.792208
209 4YB 0.416667 0.637363
210 2BA 0.41573 0.756757
211 A2P 0.41573 0.746667
212 CMP 0.41573 0.767123
213 TYR AMP 0.415094 0.725
214 AF3 ADP 3PG 0.414414 0.698795
215 2VA 0.413043 0.869565
216 AHZ 0.412844 0.682353
217 26A 0.4125 0.855072
218 2FA 0.4125 0.857143
219 6MD 0.4125 0.880597
220 G3A 0.411215 0.728395
221 7C5 0.411215 0.763158
222 AP0 0.410714 0.75
223 YLB 0.410714 0.705882
224 YLC 0.410714 0.743902
225 48N 0.409091 0.728395
226 NO7 0.408163 0.826667
227 5F1 0.407407 0.771429
228 GA7 0.407407 0.779221
229 AR6 AR6 0.407407 0.763158
230 G5P 0.407407 0.728395
231 PPS 0.40625 0.690476
232 NXX 0.405405 0.75641
233 DND 0.405405 0.75641
234 7D3 0.404494 0.730769
235 NVA 2AD 0.404255 0.821918
236 DQV 0.40367 0.776316
237 TAD 0.40367 0.719512
238 GTA 0.40367 0.702381
239 IOT 0.403509 0.697674
240 WSA 0.401786 0.659091
241 649 0.401786 0.623656
242 N37 0.401786 0.819444
243 LAQ 0.4 0.682353
244 VRT 0.4 0.833333
245 SO8 0.4 0.857143
246 HZ2 0.4 0.837838
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5dhu.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5dhu.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5DHU; Ligand: 5A8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5dhu.bio1) has 55 residues
No: Leader PDB Ligand Sequence Similarity
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